Downsampling settings

This tool applies the following downsampling settings by default.

Mode: BY_SAMPLE

To coverage: 1,000

Command-line Arguments

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify
its behavior. For example, the -L argument directs the GATK engine restricts processing
to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

GCContentByInterval specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.